Dr. Stoeckert directs the Computational Biology and Informatics Laboratory. The goal of our work is to help make sense of the enormous amount of biomedical data generated by high-throughput genomic approaches and synthesize them into something more than the sum of the parts. To that end, we are developing tools that enable researchers to mine and integrate data from a variety of different sources and types of experiments.
The first step in that process is the development of data warehouses that collect and store information in a useable fashion. In one such project, we have been working with David S. Roos, Ph.D., E. Otis Kendall Professor of Biology at Penn, and Jessica Kissinger, Ph.D., at University of Georgia, to develop a bioinformatics resource center for eukaryotic pathogens, funded by the National Institute of Allergy and Infectious Diseases. Within the resource center, we have built databases that serve research communities interested in specific pathogens. For example, PlasmoDB, houses information on the parasites that cause malaria.
To maximize the utility of data warehouses, we must have ways to represent and store data that enables researchers to make connections between experiments and between data from different types of experiments. Therefore, part of my group is involved in knowledge representation and developing ontologies, which standardizes data through the use of controlled vocabularies and relationships. Our goal is to provide the tools, including ontologies, to allow people to annotate their experiments or mark up their papers in a way that another researcher could efficiently search for and combine particular kinds of results from a variety of sources. We have been applying these to clinical epidemiological datasets available through ClinEpiDB.
We work with a number of groups on ontology projects, including the Ontology for Biomedical Investigations Consortium which is a member of the Open Biological and Biomedical Ontologies (OBO) Foundry. I have also been involved in a number of standards projects over the years, and am currently on the board of the FGED society, which promotes data sharing and standardized representation of data, particularly from genomic experiments.
The TURBO (Transforming and Unifying Research with Biomedical Ontologies) project uses the expressive power of ontologies in graph databases to represent and integrate clinical data. Powerful searches of individual medications and diagnosis codes are made possible through association to ontology classes of drug roles and diseases.
Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr, Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting: MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Research 46: D684-D691, Jan 2018.
Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ Jr, Kissinger JC, Roos DS, Hertz-Fowler C.: FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J Fungi 4(1): E39, March 2018.
Huang C, Walker EM, Dadi PK, Hu R, Xu Y, Zhang W, Sanavia T, Mun J, Liu J, Nair GG, Tan HYA, Wang S, Magnuson MA, Stoeckert CJ Jr, Hebrok M, Gannon M, Han W, Stein R, Jacobson DA, Gu G.: Synaptotagmin 4 Regulates Pancreatic β Cell Maturation by Modulating the Ca2+ Sensitivity of Insulin Secretion Vesicles. Dev Cell. 45(3): 347-361, May 2018.
Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ Jr, Spruill D, Wang H, Warrenfeltz S, Zheng J.: EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res. 45: D581-D591, January 2017 Notes:
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.: The Ontology for Biomedical Investigations. PLoS One 11(4): e0154556, April 2016.
Brochhausen M, Zheng J, Birtwell D, Williams H, Masci AM, Ellis HJ, Stoeckert CJ Jr.: OBIB-a novel ontology for biobanking. J Biomed Semantics 7: 23, May 2016.
Amanda Kuzma, Otto Valladares, Rebecca Cweibel, Emily Greenfest-Allen, Daniel M. Childress, John Malamon, Prabhakaran Gangadharan, Yi Zhao, Liming Qu, Yuk Yee Leung, Adam C. Naj, Christian J. Stoeckert Jr., Gerard D. Schellenberg, Li-San Wang: NIAGADS: The NIA Genetics of Alzheimer's Disease Data Storage Site. Alzheimer's & Dementia 12(11): 1200-1203, November 2016.
Clayton HW, Osipovich AB, Stancill JS, Schneider JD, Vianna PG, Shanks CM, Yuan W, Gu G, Manduchi E, Stoeckert CJ Jr, Magnuson MA.: Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming. Cell Rep. 17(8): 2028-2041, November 2016.
Jiang YZ, Manduchi E, Stoeckert CJ Jr, Davies PF.: Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo. BMC Genomics 16: 506, July 2015.
Gutierrez JB, Harb OS, Zheng J, Tisch DJ, Charlebois ED, Stoeckert CJ Jr, Sullivan SA.: A Framework for Global Collaborative Data Management for Malaria Research. Am J Trop Med Hyg. 93: 124-32, September 2015.
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Last updated: 12/26/2018
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